DNA barcodes discriminate freshwater fishes from the Paraba do sul River Basin, São Paulo, Brazil

Mitochondrial DNA

Volumn 22, Issue SUPPL. 1, 2011, Pages 71-79

  Pereira, Luiz H G ^a   Maia, Glucia M G ^a   Hanner, Robert ^b   Foresti, Fausto ^a   Oliveira, Claudio ^b  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSITY OF GUELPH   (Canada)

Author keywords

Biodiversity; FISH BOL; Freshwater fishes; Hidden diversity; Neotropical region; Species identification

Indexed keywords

ACCURACY; AQUATIC FAUNA; ARTICLE; BIODIVERSITY; BRAZIL; DNA BARCODING; FRESHWATER FISH; GENE SEQUENCE; GENETIC VARIABILITY; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RIVER BASIN; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; SPECIES IDENTIFICATION;

ANIMALS; BIODIVERSITY; DNA BARCODING, TAXONOMIC; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; FISHES; FRESH WATER; GENE LIBRARY; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; RIVERS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TROPICAL CLIMATE;

ASTYANAX; ASTYANAX BIMACULATUS; CHARACIDIUM; GEOPHAGUS; PISCES;

EID: 80053955400     PISSN: 19401736     EISSN: 19401744     Source Type: Journal    
DOI: 10.3109/19401736.2010.532213     Document Type: Article

References (62)

1. Ab'Saber AN. 1957. O problema das conexões antigas e da separação da drenagem do Parába e Tietê. Bol Paul Geogr 26: 38-49.
2. Ardura A, Linde AR, Moreira JC, Garcia-Vazquez E. 2010. DNA barcoding for conservation and management of Amazonian commercial fish. Biol Conserv 143:1438-1443.
3. Aron SL, Solé-Cava AM. 1991. Genetic evaluation of the taxonomic status of two varieties of the cosmopolitan ascidian Botryllus niger (Ascidiacea: Botryllidae). Biochem Syst Ecol 19: 271-276.
4. Beerkircher L, Arocha F, Barse A, Prince E, Restrepo V, Serafy J, Shivji M. 2009. Effects of species misidentification on population assessment of overfished white marlin Tetrapturus albidus and roundscale spearfish T. Georgii. Endanger Species Res 9:81-90.
5. Benine RC, Mariguela TC, Oliveira C. 2009. Nem species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae) with comments on the Moenkhausia oligolepis species complex. Neotrop Ichthyol 7(2):161-168.
6. Bizerril CRSF, Primo PBS. 2001. Peixes de águas interiores do estado do Rio de Janeiro. Rio de Janeiro: Fundação de Estudos do Mar. p 417.
7. Bortolus A. 2008. Error cascades in the biological sciences: The unwanted consequences of using bad taxonomy in ecology. Ambio 37:114-118. (Pubitemid 351656229)
8. Buckup PA, Menzes NA, Ghazzi MS. 2007. Catálogo das espécies de peixes de água doce do Brasil. 1st ed. Rio de Janeiro: Museu Nacional. p 195.
9. Castro RMC, Casatti L, Santos HF, Ferreira KM, Ribeiro AC, Benine RC, Dardis GZP, Melo ALA, Stopiglia R, Abreu TX, Bockmann FA, Carvalho M, Gibran FZ, Lima FCT. 2003. Estrutura e composição da ictiofauna de riachos do Rio Paranapanema, sudeste e sul do Brasil. Biota Neotrop 3(1): 1-31 [Online]. Available at: http://www.biotaneotropica.org.br/v3n1/pt/abstract?article \+ BN0170301.
10. Castro RMC, Casatti L, Santos HF, Melo ALA, Martins LSF, Ferreira KM, Gibran FZ, Benine RC, Carvalho M, Ribeiro AC, Abreu TX, Bockmann FA, Pelição GZ, Stopiglia R, Langeani F. 2004. Estrutura e composição da ictiofauna de riachos da bacia do Rio Grande, no Estado de São Paulo, Sudeste do Brasil. Biota Neotrop 4(1):1-39, [Online]. Available at7: http://www. biotaneotropica.org.br/v4n1/pt/abstract?article\ +BN017040 2004.
11. Castro RMC, Casatti L, Santos HF, Vari RP, Melo ALA, Martins LSF, Abreu TX, Benine RC, Gibran FZ, Ribeiro AC, Bockmann FA, Carvalho M, Pelição GZP, Ferreira KM, Stopiglia R, Akama A. 2005. Structure and composition of the stream ichthyofauna of four tributary rivers of the upper Rio Paraná basin, Brazil. Ichthyol Explor Freshw 16:193-214. (Pubitemid 41263171)
12. Costa FO, Carvalho GR. 2007. The barcode of life initiative: Synopsis and prospective societal impacts of DNA barcoding of fish. Genomics Soc Policy 3:29-40.
13. De Queiroz K. 2005. Ernst Mayr and the modern concept of species. Proc Natl Acad Sci USA 102(s1):6600-6607. (Pubitemid 40628310)
14. Diaz de Astarloa JM, Mabragana E, Hanner R, Figueroa DE. 2008. Morphological and molecular evidence for a new species of longnose skate (Rajiformes: Rajidae: Dipturus) from Argentinean waters based on DNA barcoding. Zootaxa 1921:35-46.
15. Gusmão J, Lazoski C, Solé-Cava AM. 2000. A new species of Penaeus (Crustacea: Penaeidae) revealed by allozyme and cytochrome oxidase I analyses. Mar Biol 137:435-446.
16. HajibabaeiM, De Waard JR, Ivanova NV, Ratnasingham S, Dooh R, Kirk SL, Mackie PM, Hebert PDN. 2005. Critical factors for assembling a high volume of DNA barcodes. Philos Trans R Soc B Biol Sci 360:1959-1967. (Pubitemid 44365056)
17. Hajibabei M, Singer GAC, Clare EL, Hebert PDN. 2007. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biol 5:1-15.
18. Hanner R. 2005. Proposed standards for BARCODE records in INSDC [Online]. Available at: http://www.barcoding.si.edu/PDF/DWG-data-standards-Final.pdf. Accessed on 17 July 2010.
19. Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc R Soc London B Biol Sci 270:313-321. (Pubitemid 36228536)
20. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astrapes fulgerator. Proc Natl Acad Sci USA 101:14812-14817. (Pubitemid 39410757)
21. Hubert N, Duponchelle F, Nuñez J, Garcia-Davila C, Paugy D, Renno JF. 2007. Phylogeography of the piranha genera Serrasalmus and Pygocentrus: Implications for the diversification of the Neotropical ichthyofauna. Mol Ecol 16:2115-2136. (Pubitemid 46718914)
22. Hubert N, Hanner R, HolmE, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P, Zhang J, April J, Bernatchez L. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3:e2490.
23. Ivanova NV, De Waard JR, Hebert PDN. 2006. An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol Ecol Notes 6:998-1002. (Pubitemid 44807923)
24. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. 2007. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes 7:544-548. (Pubitemid 47035520)
25. Junk W. 2007. Freshwater fishes of South America: Their biodiversity, fisheries, and habitats-a synthesis. Aquat Ecosyst Manage 10:228-242. (Pubitemid 46945315)
26. Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120. (Pubitemid 11166431)
27. Kon T, Yoshino T, Mukai T, Nishida M. 2007. DNA sequences identify numerous cryptic species of the vertebrate: A lesson from the gobioid fish Schindleria. Mol Phylogenet Evol 44: 53-62. (Pubitemid 46829912)
28. Krieger J, Fuerst PA. 2002. Evidence for a slowed rate of molecular evolution in the order Acipenseriformes. Mol Biol Evol 19: 891-897. (Pubitemid 34605988)
29. Langeani F, Castro RMC, Oyakawa OT, Shibatta OA, Pavanelli CS, Casatti L. 2007. Diversidade da fauna do Alto Rio Paraná: Composição atual e perspectivas futuras. Biota Neotrop 7: 181-197.
30. Lara A, Ponce de Leon JL, Rodriguez R, Casane D, Cote G, Bernatchez L, Garcia-Machado E. 2010. DNA barcoding of Cuban freshwater fishes: Evidence for cryptic species and taxonomic conflicts. Mol Ecol Resour 10:421-430.
31. Last PR, Gledhill DC, Holmes BH. 2007. A new handfish, Brachionichthys australis sp. nov, (Lophiiformes: Brachio-nichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacépède) . Zootaxa 1666:53-68.
32. Lemer S, Aurelle D, Vigliola L, Durand JD, Borsa P. 2007. Cytochrome b barcoding, molecular systematics and geographic differentiation in rabbitfishes (siganidae). C R Biol 330:86-94. (Pubitemid 46126735)
33. Manwell C, Baker CMA. 1963. A sibling species of seacucumber discovered by starch-gel electrophoresis. Comp Biochem Physiol 10:39-53.
34. Mendonça FF, Hashimot DT, Porto-Foresti F, Oliveira C, Gadig OBF, Foresti F. 2009. Identification of the shark species Rizoprionodon lalandii and R. porosus (Elasmobranchii: Carcharinidae) by multiplex PCR and PCR-RFLP techniques. Mol Ecol Resour 9:771-773.
35. Montoya-Burgos JI. 2003. Historical biogeography of the catfish genus Hypostomus (Siluriformes: Loricariidae), with implications on the diversification of Neotropical ichthyofauna. Mol Ecol 12: 1855-1867. (Pubitemid 36815021)
36. Moysés CB, Almeida-Toledo LF. 2002. Restriction fragment length polymorphisms of mitochondrial DNA among five freshwater fish species of the genus Astyanax (Pisces, Characidae). Genet Mol Biol 25:402-407.
37. Nelson JS. 2006. Fishes of the World. 4th ed. Hoboken, NJ: Wiley. p 601.
38. Nguyen HDT, Seifert KA. 2008. Description and DNA barcoding of three new species of Leohumicola from South Africa and the United States. Personia 21:57-98.
39. Ornelas-Garcia CP, Dominguez-Dominguez O, Doadrio I. 2008. Evolutionary history of the fish genus Astyanax Baird & Girard (1854) (Actynopterigii, Characidae) in Mesoamerica reveals multiple morphological homoplasies. BMC Evol Biol 8: 340.
40. Perdices A, Bermingham E, Montilla A, Doadrio I. 2002. Evolutionary history of the genus Rhamdia (Teleostei: Pimelo-didae) in Central America. Mol Phylogenet Evol 25:172-189. (Pubitemid 35169399)
41. Perdices A, Doadrio I, Bermingham E. 2005. Evolutionary history of the synbranchid eels (Teleostei: Synbranchidae) in Central America and the Caribbean islands inferred from their molecular phylogeny. Mol Phylogenet Evol 37:460-473. (Pubitemid 41434032)
42. Pook CE, McEwing R. 2005. Mitochondrial DNA sequences from dried snake venom: A DNA barcoding approach to the identification of venom samples. Toxicon 46:711-715. (Pubitemid 41531598)
43. Pyle RL, Earle JL, Greene BD. 2008. Five new species of the damselfish genus Chromis (Perciformes: Labroidei: Pomacen-tridae) from deep coral reefs in the tropical western Pacific. Zootaxa 1671:3-31.
44. Ratnasingham S, Hebert PDN. 2007. BOLD: The barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7: 355-364. (Pubitemid 46714172)
45. Reis RE, Ferraris C, Kullander SO. 2003. Check list of freshwater fishes of South and Central America. Porto Alegre: Edipucrs. p 729.
46. Ribeiro AC, Lima FCT, Riccomini C, Menezes NA. 2006. Fishes of the Atlantic Rainforest of Boracéia: Testimonies of the Quaternary fault reactivation within a Neoproterozoic tectonic province in Southeastern Brazil. Ichthyol Explor Freshw 17: 157-164. (Pubitemid 43881699)
47. Schaefer SA. 1998. Conflict and resolution impact of new taxa on philogenetic studies of Neotropical cascudinhos (Siluriformes: Loricariidae). In: Malabarba LR, Reis RE, Vari RP, Lucena ZMS, Lucena CAS, editors. Phylogeny and Classification of Neotropical Fishes. Porto Alegre: Edipucrs. p 375-400.
48. Shaffer HB, Thonsom RC. 2007. Delimiting species in recent radiations. Syst Biol 56:896-906.
49. Smith MA, Woodley NE, Janzen DH, Hallwachs W, Hebert PDN. 2005. DNA barcodes reveal cryptic host-specificity within the presumed polyphagus members of a genus of parasitoid flies (Diptera: Tachinidae). Proc Natl Acad Sci USA 103: 3657-3662. (Pubitemid 43376611)
50. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA 4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599. (Pubitemid 47236692)
51. Teixeira TP, Pinto BCT, Terra BF, Estiliano EO, Gracia D, Araújo FG. 2005. Diversidade das assembléias de peixes nas quatro unidades geográficas do rio Parába do Sul. Iheringia Sér Zool 95:347-357.
52. Valdez-Moreno M, Ivanova NV, Eĺas-Guitiérrez M, Contreras-Balderas S, Hebert PDN. 2009. Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. J Fish Biol 74:377-402.
53. Vari RP, Malabarba LR. 1998. Neotropical ichthyology: An overview. In: Malabarba LR, Reis RE, Vari RP, Lucena ZMS, Lucena CAS, editors. Phylogeny and classification of Neotropical fishes. Porto Alegre: Edipucrs. p 1-11.
54. Victor BC. 2007. Coryphopterus kuna, a new goby (Perciformes: Gobiidae: Gobinae) from the western Caribbean, with the identification of the late larval stage and an estimate of the pelagic larval duration. Zootaxa 1526:51-61. (Pubitemid 47094512)
55. Ward RD. 2007. DNA barcoding discriminates spurdogs of the genus Squalus. In: Last PR, White WT, Pogonoski JJ, editors. Descriptions of new dogfishies of the genus Squalus (Squaloidea: Squalidae). Hobart: CSIRO Marine and Atmospheric Research. p 130.
56. Ward RD. 2009. DNA barcode divergence within species and genera of birds and fishes. Mol Ecol Resour 9:1077-1085.
57. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philos Trans R Soc B Biol Sci 360:1847-1857. (Pubitemid 44365045)
58. Ward RD, Holmes BH, Yearsley GK. 2008. DNA barcoding reveals a likely second species of Asin sea bass (barramundi) (Lates calcarifer). J Fish Biol 72:458-463. (Pubitemid 351190161)
59. Ward RD, Hanner R, Hebert PDN. 2009. The campaign to DNA barcode all fishes. J Fish Biol 74:329-356.
60. Witt JDS, Threloff DL, Hebert PDN. 2006. DNA barcoding reveals extraordinary cryptic diversity in an amphipode genus: Implications for desert spring conservation. Mol Ecol 15: 3073-3082. (Pubitemid 44215475)
61. Yassin A, Capy P, Madi-Ravazzi L, Ogereau D, David JR. 2008. DNA barcode discovers two cryptic species and two geographical radiations in the invasive drosophilid Zaprionus indianus. Mol Ecol Resour 8:491-501. (Pubitemid 351715218)
62. Yearsley GK, Last PR. 2006. Urolophus kapalensis sp nov., a new stingaree (Myliobatiformes: Urolophidae) off eastern Australia. Zootaxa 1176:41-52. (Pubitemid 43943500)